[gmx-users] Check for bad contacts and/or reduce the timestep

Justin A. Lemkul jalemkul at vt.edu
Mon Dec 14 20:09:47 CET 2009

nishap.patel at utoronto.ca wrote:


> Steepest Descents converged to machine precision in 34 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -3.7206969e+04
> Maximum force     =  2.0111207e+04 on atom 1217
> Norm of force     =  6.9283209e+02
> I don't understand constraints I need to turn off, since I haven't 
> mentioned any in my grompp file.

This is just generic advice that mdrun provides.  The fact is your starting 
structure contains atomic overlap or clashes that cannot be resolved by energy 
minimization.  Have a look at the trajectory and see if you can get some insight 
into where things are going wrong (since problematic atom numbers are being 
printed, and perhaps re-consider how you built your system.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list